[Biojava-l] Problem with EMBL and RichStreamReader

[Antje Wollherr]

Hello biojava people,

I am new to this list and also not very familiar with BioJava. I was
trying to parse an EMBL File and extract the dna sequence with
RichSequence.IOTools.readEMBLDNA(br, ns); . 

For most of the embl files this isn't a problem, but the file with
accssion number AL009126 (Bacillus subtilis 168) caused an BioExcpetion
saying the sequence could not be read.

Can somebody tell where the problem is or how it can be solved?
I'm using BioJava 1.5.

Thank you a lot

Antje

Here is the error message:

 Exception Has Occurred During Parsing. 
Please submit the details that follow to biojava-l at biojava.org or post a
bug report to http://bugzilla.open-bio.org/ 

Format_object=org.biojavax.bio.seq.io.EMBLFormat
Accession=AL009126
Id=not set
Comments=Unable to handle contig assemblies just yet
Parse_block=
Stack trace follows ....


	at org.biojavax.bio.seq.io.EMBLFormat.readSection(EMBLFormat.java:730)
	at
org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:284)
	at
org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
	... 2 more